1. Neuroscience

Neuroscout, a unified platform for generalizable andreproducible fMRI research

  1. Alejandro de la Vega  Is a corresponding author
  2. Roberta Rocca
  3. Ross W Blair
  4. Christopher J Markiewicz
  5. Jeff Mentch
  6. James D Kent
  7. Peer Herholz
  8. Satrajit S Ghosh
  9. Russell A Poldrack
  10. Tal Yarkoni
  1. The University of Texas at Austin, United States
  2. Aarhus University, Denmark
  3. Stanford University, United States
  4. Massachusetts Institute of Technology, United States
  5. McGill University, Canada
https://doi.org/10.7554/eLife.79277
Share this article
Cite this article
  1. Alejandro de la Vega
  2. Roberta Rocca
  3. Ross W Blair
  4. Christopher J Markiewicz
  5. Jeff Mentch
  6. James D Kent
  7. Peer Herholz
  8. Satrajit S Ghosh
  9. Russell A Poldrack
  10. Tal Yarkoni
(2022)
Neuroscout, a unified platform for generalizable andreproducible fMRI research
eLife 11:e79277.
https://doi.org/10.7554/eLife.79277
  2. Download BibTeX
  3. Download .RIS

Abstract

Functional magnetic resonance imaging (fMRI) has revolutionized cognitive neuroscience, but methodological barriers limit the generalizability of findings from the lab to the real world. Here, we present Neuroscout, an end-to-end platform for analysis of naturalistic fMRI data designed to facilitate the adoption of robust and generalizable research practices. Neuroscout leverages state-of-the-art machine learning models to automatically annotate stimuli from dozens of fMRI studies using naturalistic stimuli-such as movies and narratives-allowing researchers to easily test neuroscientific hypotheses across multiple ecologically-valid datasets. In addition, Neuroscout builds on a robust ecosystem of open tools and standards to provide an easy-to-use analysis builder and a fully automated execution engine that reduce the burden of reproducible research. Through a series of meta-analytic case studies, we validate the automatic feature extraction approach and demonstrate its potential to support more robust fMRI research. Owing to its ease of use and a high degree of automation, Neuroscout makes it possible to overcome modeling challenges commonly arising in naturalistic analysis and to easily scale analyses within and across datasets, democratizing generalizable fMRI research.

Data availability

All code from our processing pipeline and core infrastructure is available online (https://www.github.com/neuroscout/neuroscout). An online supplement including all analysis code and resulting images is available as a public GitHub repository (https://github.com/neuroscout/neuroscout-paper).All analysis results are made publicly available in a public GitHub repository

The following previously published data sets were used
    1. Hanke M
    2. et al
    (2014) studyforrest
    OpenNeuro, doi:10.18112/ openneuro.ds000113 .v1.3.0.
    https://doi.org/10.18112/openneuro.ds000113.v1.3.0
    1. Nastase SA
    2. et al
    (2021) Narratives
    OpenNeuro, doi:10.18112/openneuro.ds002345 .v1.1.4.
    https://doi.org/10.18112/openneuro.ds002345.v1.1.4

Article and author information

Author details

  1. Alejandro de la Vega

    Department of Psychology, The University of Texas at Austin, Austin, United States
    For correspondence
    delavega@utexas.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9062-3778

  2. Roberta Rocca

    Interacting Minds Centre, Aarhus University, Aarhus, Denmark
    Competing interests
    The authors declare that no competing interests exist.

  3. Ross W Blair

    Department of Psychology, Stanford University, Stanford, United States
    Competing interests
    The authors declare that no competing interests exist.

  4. Christopher J Markiewicz

    Department of Psychology, Stanford University, Stanford, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6533-164X

  5. Jeff Mentch

    McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.

  6. James D Kent

    Department of Psychology, The University of Texas at Austin, Austin, United States
    Competing interests
    The authors declare that no competing interests exist.

  7. Peer Herholz

    Montreal Neurological Institute, McGill University, Montreal, Canada
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9840-6257

  8. Satrajit S Ghosh

    McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5312-6729

  9. Russell A Poldrack

    Department of Psychology, Stanford University, Stanford, United States
    Competing interests
    The authors declare that no competing interests exist.

  10. Tal Yarkoni

    Department of Psychology, The University of Texas at Austin, Austin, United States
    Competing interests
    The authors declare that no competing interests exist.

Funding

National Institute of Mental Health (R01MH109682)

  • Alejandro de la Vega
  • Roberta Rocca
  • Ross W Blair
  • Christopher J Markiewicz
  • Jeff Mentch
  • James D Kent
  • Peer Herholz
  • Satrajit S Ghosh
  • Russell A Poldrack
  • Tal Yarkoni

National Institute of Mental Health (R01MH096906)

  • Alejandro de la Vega
  • James D Kent
  • Tal Yarkoni

National Institute of Mental Health (R24MH117179)

  • Peer Herholz
  • Satrajit S Ghosh

National Institute of Mental Health (R24MH117179)

  • Ross W Blair
  • Christopher J Markiewicz
  • Russell A Poldrack

Canada First Research Excellence Fund

  • Peer Herholz

Brain Canada Fondation

  • Peer Herholz

Unifying Neuroscience and Artificial Intelligence - Québec

  • Peer Herholz

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

© 2022, de la Vega et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 1,376
    views
  • 236
    downloads
  • 6
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Alejandro de la Vega
  2. Roberta Rocca
  3. Ross W Blair
  4. Christopher J Markiewicz
  5. Jeff Mentch
  6. James D Kent
  7. Peer Herholz
  8. Satrajit S Ghosh
  9. Russell A Poldrack
  10. Tal Yarkoni
(2022)
Neuroscout, a unified platform for generalizable andreproducible fMRI research
eLife 11:e79277.
https://doi.org/10.7554/eLife.79277

Share this article

https://doi.org/10.7554/eLife.79277

Categories and tags

Research organism

Further reading

    1. Neuroscience

    Cerebellar Purkinje cells control posture in larval zebrafish (Danio rerio)

    Franziska Auer, Katherine Nardone ... David Schoppik
    Research Article

    Cerebellar dysfunction leads to postural instability. Recent work in freely moving rodents has transformed investigations of cerebellar contributions to posture. However, the combined complexity of terrestrial locomotion and the rodent cerebellum motivate new approaches to perturb cerebellar function in simpler vertebrates. Here, we adapted a validated chemogenetic tool (TRPV1/capsaicin) to describe the role of Purkinje cells — the output neurons of the cerebellar cortex — as larval zebrafish swam freely in depth. We achieved both bidirectional control (activation and ablation) of Purkinje cells while performing quantitative high-throughput assessment of posture and locomotion. Activation modified postural control in the pitch (nose-up/nose-down) axis. Similarly, ablations disrupted pitch-axis posture and fin-body coordination responsible for climbs. Postural disruption was more widespread in older larvae, offering a window into emergent roles for the developing cerebellum in the control of posture. Finally, we found that activity in Purkinje cells could individually and collectively encode tilt direction, a key feature of postural control neurons. Our findings delineate an expected role for the cerebellum in postural control and vestibular sensation in larval zebrafish, establishing the validity of TRPV1/capsaicin-mediated perturbations in a simple, genetically tractable vertebrate. Moreover, by comparing the contributions of Purkinje cell ablations to posture in time, we uncover signatures of emerging cerebellar control of posture across early development. This work takes a major step towards understanding an ancestral role of the cerebellum in regulating postural maturation.

    1. Neuroscience

    Accelerated signal propagation speed in human neocortical dendrites

    Gáspár Oláh, Rajmund Lákovics ... Gábor Tamás
    Research Article

    Human-specific cognitive abilities depend on information processing in the cerebral cortex, where the neurons are significantly larger and their processes longer and sparser compared to rodents. We found that, in synaptically connected layer 2/3 pyramidal cells (L2/3 PCs), the delay in signal propagation from soma to soma is similar in humans and rodents. To compensate for the longer processes of neurons, membrane potential changes in human axons and/or dendrites must propagate faster. Axonal and dendritic recordings show that the propagation speed of action potentials (APs) is similar in human and rat axons, but the forward propagation of excitatory postsynaptic potentials (EPSPs) and the backward propagation of APs are 26 and 47% faster in human dendrites, respectively. Experimentally-based detailed biophysical models have shown that the key factor responsible for the accelerated EPSP propagation in human cortical dendrites is the large conductance load imposed at the soma by the large basal dendritic tree. Additionally, larger dendritic diameters and differences in cable and ion channel properties in humans contribute to enhanced signal propagation. Our integrative experimental and modeling study provides new insights into the scaling rules that help maintain information processing speed albeit the large and sparse neurons in the human cortex.

    1. Neuroscience

    Cognition: When working memory works for our goals

    Jacob A Miller
    Insight

    When navigating environments with changing rules, human brain circuits flexibly adapt how and where we retain information to help us achieve our immediate goals.